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Class-directed structure determination: Foundation for a protein structure initiative

Class-directed structure determination: Foundation for a protein structure initiative,10.1002/pro.5560070901,Protein Science,Thomas C. Terwilliger,Geo

Class-directed structure determination: Foundation for a protein structure initiative   (Citations: 36)
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Journal: Protein Science - PROTEIN SCI , vol. 7, no. 9, pp. 1851-1856, 1998
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    • ...Proteins from a pathogen Potential drug targets Proteins from a thermophile Robust enzyme (3) Large-scale targets...
    • ...The criteria used to select these “easy” proteins were (1) sizes of <50 kDa; (2) were possible candidates for molecular replacement; (3) were not part of a complex; (4) did not contain signal peptides or transmembrane regions; and (5) were predicted to be soluble, based on the near absence of disordered regions...

    Enrique E. Abolaet al. The Importance of Target Selection Strategies in Structural Biology

    • ... of 37,000 structures in the PDB library (many are redundant),6 four million models/foldassignments can be obtained by a simple combination of the PSI-Blast search and the comparative modeling technique.7 Development of more sophisticated and automated computer modeling approach will dramatically enlarge the scope of modelable proteins in the structuregenomics project.8 The critical problems/efforts in the field include the following: (1) ...
    • ...The four parameters, c1, c2 in Eq. (1), the gap opening penalty (c3), and the gap extension penalty (c4) are decided by trial and error on the ProSup benchmark.31 Depending on the profiles generated from PSI-Blast or HMM search and the alignment search by the NW global or SW local dynamic programming algorithms, four complementary PPA threading alignments are used in the consequent I-TASSER assembly...
    • ...The human section prediction uses essentially the same procedure, except for the following differences: (1) the domain border assignment has been made based on visual view of the 1D threading sequence alignments and 3D template structures, which are further adjusted by the CASP7 domain server predictions from Robetta-Ginzu41 and Ma-OPUS-DOM; (2) for the hard targets that have no strong PPA hit with a Z-score > 7, additional alignments ...
    • ...(1) For hard targets when PPA programs have no confident hit, we exploited multiple threading templates from the CASP7 servers...
    • ...Compared with the original version of TASSER,14,22,23 new components include: (1) a new set of secondary structure confined PPA threading programs are developed; (2) new energy terms including neural network solvent accessibility predictions are incorporated and reparameterized on the basis of structure decoys in different categories; (3) a two-round progressive assembly simulation is developed for removing structure clashes and refining ...

    Yang Zhang. Template-based modeling and free modeling by I-TASSER in CASP7

    • ...The identification of the interaction sites in protein structures is a critical step in the determination of function from the wealth of sequence and structure information emerging from genome sequencing and from structural genomics efforts [8-14]...

    Ying Weiet al. Selective prediction of interaction sites in protein structures with T...

    • ...functional genomics (Kim 1998; Sali 1998; Terwilliger et al 1998; Burley et al 1999; Mittl and Grutter 2001)...

    Edward N Bakeret al. Protein structure prediction and analysis as a tool for functional gen...

    • ...One of the main goals of post-genomic research is to determine the three-dimensional (3D) structure of the complete proteome of an organism, starting by solving the structures that have little or no sequence similarity to proteins of known structure (Montelione and Anderson, 1999; Terwilliger et al., 1998)...

    Ernesto Estrada. Characterization of the folding degree of proteins

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